| Variant ID: vg0114587405 (JBrowse) | Variation Type: SNP |
| Chromosome: chr01 | Position: 14587405 |
| Reference Allele: G | Alternative Allele: T |
| Primary Allele: G | Secondary Allele: T |
Inferred Ancestral Allele : G (evidence from allele frequency in Oryza rufipogon: G: 1.00, others allele: 0.00, population size: 245. )
AATTCTACTGCTTTATGCATAAAAATTGTTTAAGCATCTCAATGTATCAAATGTTAACCAAAACTAAACTGAAGCGGTTAAATAAGCTTTTTTTTTTATT[G/T]
CTGAAGAGTACATTAATTTAAGTGTTGCATTCATGGTAAGAACAAGAACAACTATACAGAGTTTTTGTATGTACGAAGTTGAGTACTCACATATGTCAAC
GTTGACATATGTGAGTACTCAACTTCGTACATACAAAAACTCTGTATAGTTGTTCTTGTTCTTACCATGAATGCAACACTTAAATTAATGTACTCTTCAG[C/A]
AATAAAAAAAAAAGCTTATTTAACCGCTTCAGTTTAGTTTTGGTTAACATTTGATACATTGAGATGCTTAAACAATTTTTATGCATAAAGCAGTAGAATT
| Populations | Population Size | Frequency of G(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 77.80% | 1.60% | 0.91% | 19.72% | NA |
| All Indica | 2759 | 65.80% | 0.00% | 0.94% | 33.27% | NA |
| All Japonica | 1512 | 94.00% | 4.80% | 1.06% | 0.13% | NA |
| Aus | 269 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Indica I | 595 | 50.90% | 0.00% | 0.67% | 48.40% | NA |
| Indica II | 465 | 71.20% | 0.00% | 0.22% | 28.60% | NA |
| Indica III | 913 | 70.90% | 0.00% | 1.20% | 27.93% | NA |
| Indica Intermediate | 786 | 67.90% | 0.00% | 1.27% | 30.79% | NA |
| Temperate Japonica | 767 | 99.60% | 0.10% | 0.26% | 0.00% | NA |
| Tropical Japonica | 504 | 82.90% | 14.30% | 2.58% | 0.20% | NA |
| Japonica Intermediate | 241 | 99.20% | 0.00% | 0.41% | 0.41% | NA |
| VI/Aromatic | 96 | 100.00% | 0.00% | 0.00% | 0.00% | NA |
| Intermediate | 90 | 84.40% | 1.10% | 1.11% | 13.33% | NA |
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0114587405 | G -> T | LOC_Os01g25730.1 | downstream_gene_variant ; 4027.0bp to feature; MODIFIER | silent_mutation | Average:62.957; most accessible tissue: Zhenshan97 young leaf, score: 78.644 | N | N | N | N |
| vg0114587405 | G -> T | LOC_Os01g25740.1 | intron_variant ; MODIFIER | silent_mutation | Average:62.957; most accessible tissue: Zhenshan97 young leaf, score: 78.644 | N | N | N | N |
| vg0114587405 | G -> DEL | N | N | silent_mutation | Average:62.957; most accessible tissue: Zhenshan97 young leaf, score: 78.644 | N | N | N | N |